.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/plot_protonation.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_plot_protonation.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_plot_protonation.py:


Parse, protonate and round-trip a molecule
==========================================

This offline example uses ethanol from Biotite's bundled CCD. The same code runs
against the installed core wheel in CI, without PyTorch or a PDB mirror.

.. GENERATED FROM PYTHON SOURCE LINES 8-20

.. code-block:: Python


    from pathlib import Path
    from tempfile import TemporaryDirectory

    import numpy as np

    from atomworks.experimental.protonation import assign_hydrogens, place_hydrogens
    from atomworks.io import parse
    from atomworks.io.config import ParseConfig
    from atomworks.io.utils.ccd import get_ccd_component_from_biotite
    from atomworks.io.utils.io_utils import to_cif_file








.. GENERATED FROM PYTHON SOURCE LINES 21-22

Prepare a heavy-atom input and parse it with explicit configuration.

.. GENERATED FROM PYTHON SOURCE LINES 22-49

.. code-block:: Python

    component = get_ccd_component_from_biotite("EOH")
    component.chain_id[:] = "A"
    component.res_id[:] = 1
    component.hetero[:] = True
    heavy = component[component.element != "H"]
    config = ParseConfig.from_preset("minimal", hydrogen_policy="keep", add_id_and_entity_annotations=True)

    with TemporaryDirectory() as directory:
        path = Path(directory) / "ethanol.cif"
        to_cif_file(heavy, path, ccd_entries={"EOH": component})
        atoms = parse(path, config=config)["asym_unit"][0]

        # Assignment chooses the state; placement supplies hydrogen coordinates.
        state = assign_hydrogens(atoms, ph=7.4)
        protonated = place_hydrogens(state)
        np.testing.assert_array_equal(protonated.coord[protonated.element != "H"], atoms.coord)
        assert np.count_nonzero(protonated.element == "H") == 6
        assert np.isfinite(protonated.coord).all()

        # Write and reparse the complete molecule without changing its chemistry.
        to_cif_file(protonated, path, ccd_entries={"EOH": component})
        restored = parse(path, config=config)["asym_unit"][0]
        np.testing.assert_array_equal(restored.atom_name, protonated.atom_name)
        np.testing.assert_allclose(restored.coord, protonated.coord, atol=0.001)
        np.testing.assert_array_equal(restored.bonds.as_array(), protonated.bonds.as_array())

    print("Ethanol: 3 heavy atoms and 6 hydrogens; coordinates and bonds round-trip.")




.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    Writing chem_comp with chem_comp_source='ccd' from a plain AtomArray. A plain AtomArray has no preserved CCD context, so known component codes resolve to the bundled CCD. If this structure came from a CIF, parse it with return_atom_array_plus=True to preserve its CCD registry. If it was constructed or modified and a component slice is the complete intended CCD definition, write it with ccd_entries={code: component_template}; run any earlier CCD-dependent processing inside `with custom_ccd_residues(ccd_entries):`. Silence this warning with CIFWriteConfig(warn_on_ccd_without_registry=False).
    Ethanol: 3 heavy atoms and 6 hydrogens; coordinates and bonds round-trip.





.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 1.182 seconds)


.. _sphx_glr_download_auto_examples_plot_protonation.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_protonation.ipynb <plot_protonation.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_protonation.py <plot_protonation.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_protonation.zip <plot_protonation.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_